NM_021116.4:c.1450-5G>T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_021116.4(ADCY1):c.1450-5G>T variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.012 in 1,613,326 control chromosomes in the GnomAD database, including 169 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_021116.4 splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADCY1 | NM_021116.4 | c.1450-5G>T | splice_region_variant, intron_variant | Intron 7 of 19 | ENST00000297323.12 | NP_066939.1 | ||
ADCY1 | NM_001281768.2 | c.775-5G>T | splice_region_variant, intron_variant | Intron 8 of 9 | NP_001268697.1 | |||
ADCY1 | XM_005249584.4 | c.1450-5G>T | splice_region_variant, intron_variant | Intron 7 of 18 | XP_005249641.1 | |||
ADCY1 | XM_005249585.3 | c.1450-5G>T | splice_region_variant, intron_variant | Intron 7 of 8 | XP_005249642.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADCY1 | ENST00000297323.12 | c.1450-5G>T | splice_region_variant, intron_variant | Intron 7 of 19 | 1 | NM_021116.4 | ENSP00000297323.7 | |||
ADCY1 | ENST00000432715.5 | c.775-5G>T | splice_region_variant, intron_variant | Intron 8 of 9 | 2 | ENSP00000392721.1 | ||||
ADCY1 | ENST00000621543.1 | c.775-5G>T | splice_region_variant, intron_variant | Intron 7 of 8 | 5 | ENSP00000479770.1 | ||||
ADCY1 | ENST00000646653.1 | n.391-5G>T | splice_region_variant, intron_variant | Intron 3 of 7 |
Frequencies
GnomAD3 genomes AF: 0.0115 AC: 1747AN: 152138Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.0126 AC: 3152AN: 250766Hom.: 42 AF XY: 0.0125 AC XY: 1699AN XY: 135474
GnomAD4 exome AF: 0.0121 AC: 17612AN: 1461070Hom.: 153 Cov.: 31 AF XY: 0.0120 AC XY: 8738AN XY: 726768
GnomAD4 genome AF: 0.0115 AC: 1745AN: 152256Hom.: 16 Cov.: 32 AF XY: 0.0118 AC XY: 882AN XY: 74442
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
c.1450-5G>T in intron 7 of ADCY1: This variant is not expected to have clinical significance because it has been identified in 1.66% (1102/66292) of European ch romosomes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute. org; dbSNP rs77524127). -
ADCY1-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at